Ontogenetic changes in the ecological requirements of fishes are thought to influence intraspecific patterns of occurrence and abundance, yet patterns of variation in the distribution of different cohorts are unknown for many species. In prairie stream headwaters with variable habitats, we predict cohort occurrences, densities, and juvenile growth rates to vary considerably over both space and time. Specifically, the differences in abiotic factors across sites will likely affect the occurrence and growth of different age classes. To evaluate factors associated with cohort structure, we evaluated population dynamics of two cyprinid species, central stoneroller Campostoma anomalum and southern redbelly dace Chrosomus erythrogaster, using a long-term monitoring data set that included six sites sampled semiannually for 8 to 14 years. Densities of adult stoneroller were higher in pools while juveniles had higher densities in riffles, leading to within-site spatial differences in the occurrence of each age class. Across-site habitats also varied in the occurrence of different age classes of stonerollers, with sites being either suitable for both adults and juveniles, specialized for one age class, or temporally variable for both age classes. In contrast to stonerollers, all age classes of dace were pool specialists with constantly high occurrences of both age classes during all times of the year. Age-specific growth, for both species, did not vary across sites, but growth was higher for stonerollers during wet years compared with drier years at two sites. Headwater streams provide important habitat for many fishes, but the use of age-specific habitats is variable among species and likely driven by species traits as well as biotic and abiotic characteristics of those habitats.